Hepatitis C virus (HCV) is a member of the hepacivirus genus in the family Flaviviridae. It is the major causative agent of non-A, non-B viral hepatitis and is the major cause of transfusion-associated hepatitis and accounts for a significant proportion of hepatitis cases worldwide. Although acute HCV infection is often asymptomatic, nearly 80% of cases resolve to chronic hepatitis. The persistent property of the HCV infection has been explained by its ability to escape from the host immune surveillance through hypermutability of the exposed regions in the envelope protein E2 (Weiner et al., Virology 180:842-848 (1991); Weiner et al. Proc. Natl. Acad. Sci. USA 89:3468-3472 (1992). About 60% of patients develop liver disease with various clinical outcomes ranging from an asymptomatic carrier state to chronic active hepatitis and liver cirrhosis (occurring in about 20% of patients), which is strongly associated with the development of hepatocellular carcinoma (occurring in about 1-5% of patients) (for reviews, see Cuthbert, Clin. Microbiol. Rev. 7:505-532 (1994); World Health Organization, Lancet 351:1415 (1998). The World Health Organization estimates that 170 million people are chronically infected with HCV, with an estimate of 4 million of these living in the United States.
HCV is an enveloped RNA virus containing a single-stranded positive-sense RNA genome approximately 9.5 kb in length (Choo et al., Science 244:359-362 (1989)). The RNA genome contains a 5′-nontranslated region (5′ NTR) of 341 nucleotides (Brown et al., Nucl. Acids Res. 20:5041-5045 (1992); Bukh et al., Proc. Natl. Acad. Sci. USA 89:4942-4946 (1992)), a large open reading frame (ORF) encoding a single polypeptide of 3,010 to 3,040 amino acids (Choo et al. (1989), supra;), and a 3′-nontranslated region (3′-NTR) of variable length of about 230 nucleotides (Kolykhalov et al., J. Virol. 70:3363-3371 (1996); Tanaka et al., J. Virol. 70:3307-3312 (1996)). By analogy to other plus-strand RNA viruses, the 3′ nontranslated region is assumed to play an important role in viral RNA synthesis. HCV is similar in amino acid sequence and genome organization to flaviviruses and pestiviruses (Miller et al., Proc. Natl. Acad. Sci. USA 87:2057-2061 (1990)), and therefore HCV has been classified as a third genus of the family Flaviviridae (Francki et al., Arch. Virol. 2:223-233 (1991).
Studies of HCV replication and the search for specific anti-HCV agents have been hampered by the lack of an efficient tissue culture system for HCV propagation, the absence of a suitable small-animal model for HCV infection, the low level of viral replication, and the considerable genetic heterogeneity associated with the virus (Bartenschlager, Antivir. Chem. Chemother. 8:281-301 (1997); Simmonds et al., J. Gen. Virol. 74:2391-2399 (1993)). The current understanding of the structures and functions of the HCV genome and encoded proteins is primarily derived from in vitro studies using various recombinant systems (Bartenschlager (1997), supra).
The 5′ NTR is one of the most conserved regions of the viral genome and plays a pivotal role in the initiation of translation of the viral polyprotein (Bartenschlager (1997), supra). A single long ORF encodes a polyprotein, which is co- or post-translationally processed into structural (core, E1, and E2) and nonstructural (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) viral proteins by either cellular or viral proteinases (Bartenschlager (1997), supra). The 3′ NTR consists of three distinct regions: a variable region of about 38 nucleotides following the stop codon of the polyprotein, a polyuridine tract of variable length with interspersed substitutions of cytidines, and 98 nucleotides (nt) at the very 3′ end which are highly conserved among various HCV isolates. The order of the genes within the genome is: NH2—C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B-COOH (Grakoui et al., J. Virol. 67:1385-1395 (1993)).
Processing of the structural proteins core (C), envelope protein 1 and (E1, E2), and the p7 region is mediated by host signal peptidases. In contrast, maturation of the nonstructural (NS) region is accomplished by two viral enzymes. The HCV polyprotein is first cleaved by a host signal peptidase generating the structural proteins C/E1, E1/E2, E2/p7, and p7/NS2 (Hijikata et al., Proc. Natl. Acad. Sci. USA 88:5547-5551 (1991); Lin et al., J. Virol. 68:5063-5073 (1994)). The NS2-3 proteinase, which is a metalloprotease, then cleaves at the NS2/NS3 junction. The NS3/4A proteinase complex (NS3 being a serine protease and NS4A acting as a cofactor of the NS3 protease), is then responsible for processing at all the remaining sites (Bartenschlager et al., J. Virol. 67:3835-3844 (1993); Bartenschlager (1997), supra). RNA helicase and NTPase activities have also been identified in the NS3 protein. The N-terminal one-third of the NS3 protein functions as a protease, and the remaining two-thirds of the molecule acts as the helicase/ATPase that is thought to be involved in HCV replication (Bartenschlager (1997), supra). NS5A may be phosphorylated and act as a putative cofactor of NS5B. The fourth viral enzyme, NS5B, is an RNA-dependent RNA polymerase (RdRp) and a key component responsible for replication of the viral RNA genome (Lohmann et al., J. Virol. 71:8416-8428 (1997)). NS5B contains the “GDD” sequence motif, which is highly conserved among all RdRps characterized to date (Poch et al., EMBO J. 8:3867-3874 (1989)).
Replication of HCV is thought to occur in membrane-associated replication complexes. Within these, the genomic plus-strand RNA is transcribed into minus-strand RNA, which in turn can be used as a template for synthesis of progeny genomic plus strands. At least two viral proteins appear to be involved in this reaction: the NS3 protein, which carries in the carboxy terminal two-thirds a nucleoside triphosphatase/RNA helicase, and the NS5B protein, which is a membrane-associated phosphoprotein with an RNA-dependent RNA polymerase activity (RdRp) (Hwang et al., J. Virol. 227:439-446 (1997)). While the role of NS3 in RNA replication is less clear, NS5B apparently is the key enxyme responsible for synthesis of progeny RNA strands. Using recombinant baculoviruses to express NS5B in insect cells and a synthetic nonviral RNA as a substrate, two enzymatic activities have been identified as being associated with it: a primer-dependent RdRp and a terminal transferase (TNTase) activity. It was subsequently confirmed and further characterized through the use of the HCV RNA genome as a substrate (Lohmann et al., Virology 249:108-118 (1998)). Recent studies have shown that NS5B with a C-terminal 21 amino-acid truncation expressed in Escherichia coli is also active for in vitro RNA synthesis (Ferrari et al., J. Virol. 73:1649-1654 (1999); Yamashita et al., J. Biol. Chem. 273:15479-15486 (1998)).
Since persistent infection of HCV is related to chronic hepatitis and eventually to hepatocarcinogenesis, HCV replication is one of the targets to eradicate HCV reproduction and to prevent hepatocellular carcinoma. Unfortunately, present treatment approaches for HCV infection are characterized by relatively poor efficacy and an unfavorable side-effect profile. Therefore, intensive effort is directed at the discovery of molecules to treat this disease. These new approaches include the development of prophylactic and therapeutic vaccines, the identification of interferons with improved pharmacokinetic characteristics, and the discovery of drugs designed to inhibit the function of three major viral proteins: protease, helicase and polymerase. Also, the HCV RNA genome itself, particularly the IRES element, is being actively exploited as an antiviral target using antisense molecules and catalytic ribozymes. For a review, see Wang et al., Prog. Drug Res. 55:1-32 (2000).
Particular therapies for HCV infection include α-interferon alone and the combination of α-interferon with ribavirin. These therapies have been shown to be effective in a portion of patients with chronic HCV infection (Marcellin et al., Ann. Intern. Med. 127:875-881 (1997); Zeuzem et al., Hepatology 28:245-252 (1998)). Use of antisense oligonucleotides for treatment of HCV infection has also been proposed (Anderson et al., U.S. Pat. No. 6,174,868 (2001)) as well as use of free bile acids, such as ursodeoxycholic acid and chenodeoxycholic acid, or conjugated bile acids, such as tauroursodeoxycholic acid (Ozeki, U.S. Pat. No. 5,846,964 (1998)). Phosphonoformic acid esters have also been proposed to be useful in treating a number of viral infections including HCV (Helgstrand et al., U.S. Pat. No. 4,591,583 (1986)). Vaccine development has been hampered by the high degree of immune evasion and the lack of protection against reinfection, even with the same inoculum (Wyatt et al., J. Virol. 72:1725-1730 (1998)).
The development of small-molecule inhibitors directed against specific viral targets has become a focus of anti-HCV research. The determination of crystal structures for NS3 protease (Kim et al., Cell 87:343-355 (1996); Love et al., Cell 87:331-342 (1996)) and NS3 RNA helicase (Kim et al. Structure 6:89-100 (1998)) has provided important structural insights for rational design of specific inhibitors.
NS5B, the RNA-dependent RNA polymerase, is also a useful viral target for small-molecule inhibitors. Studies with pestiviruses have shown that the small compound VP32947 (3-[((2-dipropylamino)ethyl)thio]-5H-1,2,4-triazino[5,6-b]indole) is a potent inhibitor of pestivirus replication and most likely inhibits the NS5B enzyme since resistant strains are mutated in this gene (Baginski et al., Proc. Natl. Acad. Sci. USA 97:7981-7986 (2000)). Inhibition of RdRp activity by (−)β-L-2′,3′-dideoxy-3′-thiacytidine 5′-triphosphate (3TC; lamivudine triphosphate) and phosphonoacetic acid also has been observed (Ishii et al., Hepatology 29:1227-1235 (1999)).
Nonetheless, there is still a need for non-peptide, small-molecule compounds that are HCV RdRp inhibitors and that have desirable or improved physical and chemical properties appropriate for pharmaceutical applications.